Rcwl/RcwlPipelines: Use R To Build, Read, Write, And execute CWL Workflows"

Instructor(s) name(s) and contact information

• Qian Liu ([email protected]) twitter
• Slack channel: community-bioc/#rcwl

Workshop Description

The Common Workflow Language (CWL) is used to provide portable and reproducible data analysis workflows across different tools and computing environments. We have developed Rcwl, an R interface to CWL, to provide easier development, use and maintenance of CWL pipelines from within R. We have also collected nearly 200 pre-built tools and pipelines in RcwlPipelines, ready to be queried and used by researchers in their own analysis.

Here we included a scRNAseq preprocessing pipeline which uses STARsolo for alignment and quantification, and DropletUtils to load the data into R as an singleCellExperiment object. This pipeline demonstrates the typical use case of our packages.

For the demo, users also need to install the following packages:

BiocManager::install(c("rworkflow/Rcwl", "rcwlwork/RcwlPipelines", 
	                "git2r", "DropletUtils", "BiocParallel"))